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LiDAR Is Effective in Characterizing Vine Growth and Detecting Associated Genetic Loci

Plant Phenomics 2023年第4期5卷 836-851页

作者： Elsa Chedid Komlan Avia Vincent Dumas Lionel Ley Nicolas Reibel Gisèle Butterlin Maxime Soma Raul Lopez-Lozano Frédéric Baret Didier Merdinoglu Éric Duchêne INRAE University of StrasbourgUMR SVQV28rue de Herrlisheim68000 ColmarFrance INRAE UEAV28rue de Herrlisheim68000 ColmarFrance INRAE Aix-Marseille UniversitéUMR RECOVER3275 Route de Cézanne13182 Aix-en-ProvenceFrance INRAE Avignon UniversitéUMR EMMAHUMT CAPTE228route de l'aérodrome84914 AvignonFrance

The strong societal demand to reduce pesticide use and adaptation to climate change challenges the capacities of phenotyping new varieties in the vineyard.High-throughput phenotyping is a way to obtain meaningful and reliable information on hundreds of genotypes in a limited period.We evaluated traits related to growth in 209 genotypes from an interspecific grapevine biparental cross,between IJ119,a local genitor,and Divona,both in summer and in winter,using several methods:fresh pruning wood weight,exposed leaf area calculated from digital images,leaf chlorophyll concentration,and LiDAR-derived apparent volumes.Using high-density genetic information obtained by the genotyping by sequencing technology(GBS),we detected 6 regions of the grapevine genome[quantitative trait loci(QTL)]associated with the variations of the traits in the progeny.The detection of statistically significant QTLs,as well as correlations(R^(2))with traditional methods above 0.46,shows that LiDAR technology is effective in characterizing the growth features of the grapevine.Heritabilities calculated with LiDAR-derived total canopy and pruning wood volumes were high,above 0.66,and stable between growing seasons.These variables provided genetic models explaining up to 47%of the phenotypic variance,which were better than models obtained with the exposed leaf area estimated from images and the destructive pruning weight measurements.Our results highlight the relevance of LiDAR-derived traits for characterizing genetically induced differences in grapevine growth and open new perspectives for high-throughput phenotyping of grapevines in the vineyard.

关键词： LiDAR traits hundreds

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Generic classification of Asian horned toads(Anura:Megophryidae: Megophryinae) and monograph of Chinese species

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Zoological Research 2023年第2期44卷 380-450页

作者： Zhi-Tong Lyu Shuo Qi Jian Wang Si-Yu Zhang Jian Zhao Zhao-Chi Zeng Han Wan Jian-Huan Yang Yun-Ming Mo Ying-Yong Wang State Key Laboratory of Biocontrol/The Museum of Biology School of Life Sciences/School of EcologySun Yat-sen UniversityGuangzhouGuangdong 510275China State Key Laboratory of Genetic Resources and Evolution&Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China Kadoorie Conservation China Kadoorie Farm and Botanic GardenTai PoHong Kong SARChina Natural History Museum of Guangxi NanningGuangxi 530012China

The subfamily Megophryinae,as a representative batrachian group of the Oriental Realm and one of the most diverse groups of amphibians,has attracted considerable attention due to continued conjecture regarding its generic classification and failure to reach a satisfactory consensus.China boasts the richest diversity of Asian horned toads,containing some two thirds of the total species cataloged.However,most species have a complicated taxonomic history,resulting in multiple misidentifications.As such,an overall clarification of historical records and regional checklists is required.In the current investigation,we established the phylogeny of the Asian horned toads and performed detailed examinations with redefinitions of several important morphological traits.Based on the phylogenetic relationships and morphological differences,we propose a new ten-genus classification for the Asian horned toad subfamily Megophryinae:i.e.,Brachytarsophrys,Atympanophrys,Grillitschia,Sarawakiphrys gen.nov.,Jingophrys gen.nov.,Xenophrys,Megophrys,Pelobatrachus,Ophryophryne,and Boulenophrys.Revisions on the diagnosability,distribution,and content of each genus are provided.Furthermore,we present a careful review of the taxonomic history of Asian horned toad species from China and provide a monograph of congeners,including six species of Brachytarsophrys,four species of Atympanophrys,five species of Jingophrys gen.nov.,10 species of Xenophrys,two species of Ophryophryne,and 60 species of Boulenophrys.Finally,we discuss the importance of traditional morphological traits based on multiple populations in taxonomic work as well as taxonomic inflation caused by the genetic species delimitation.

关键词： traits phylogeny continued

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Analysis of quantitative trait loci underlying the traits related to chlorophyll content of the flag leaf in rice

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Frontiers in Biology 2008年第4期3卷 443-448页

作者： Guohua YANG Sansi TU Shaoqing LI Lingling FENG Jin KONG Hui LI Yangsheng LI College of Life Sciences Wuhan University Key Laboratory of the Ministry of Education for Plant Developmental BiologyWuhan 430072China

A population of 117 doubled haploid(DH)lines derived from the cross of Zhaiyeqing 8(indica)6 Jingxi 17(japonica)was employed to map quantitative trait loci(QTL)underlying four physiological traits related to chlorophyll contents of the flag leaf.There were significantly positive correlations among chlorophyll a,chlorophyll b and chlorophyll a+b content.Chlorophyll a/b ratio was significantly negatively correlated with chlorophyll b content.These four traits were normally distributed with transgressive segregation,suggesting that they were controlled by multiple minor genes.A total of 11 QTLs were detected for the four traits and they lay on six chromosomes.Each of them explained 9.2%–19.6%of the phenotypic variations,respectively.Of these,two QTLs controlling chlorophyll a content were mapped on chromosomes 2 and 5;four QTLs underlying chlorophyll b content were mapped on chromosomes 2,3,5 and 9;three QTLs underlying chlorophyll a+b amount were mapped on chromosomes 3,5 and 9;two QTLs underlying chlorophyll a/b ratio were mapped on chromosomes 6 and 11.The intrinsic relationship among the four traits and the practical implication in rice breeding are discussed.

关键词： rice chlorophyll traits quantitative trait loci(QTL) correlation breeding

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ANALYSIS OF GENETIC CORRELATIONS FOR QUALITY traits IN INDICA RICE

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生物数学学报 1995年第3期10卷 15-20页

作者： Chunhai Shi Jun Zhu(Agronomy Department,Zhejiang Agricultural University,Hangzhou 310029)

Analysis of genetic correlations was conducted for cooking and nutrient quality traits of milled rice in indica rice(Oryza sativa L.subsp.indicc)by using a genetic model for endosperm traits of cereal crops.It was indicated by the results that the relationships between gel consistency and protein content,protein content and the ratio of lysine content to protein content,and protein index and the ratio of lysine content to protein content were mainly controlled by additive effects,but also affected by some dominanceeffects.The genetic correlations between amylose content and lysine content,gel consistency and protein index,and between gel consistency and the ratio of lysine content to protein content showed that relationships for these traits were mainly controlled by some dominance effects.Indirect selection for those traits controlled mainly by additive correlations was better than those mainly controlled by dominance correlations.The results in this experiment could be used in rice breeding.

关键词： Genetic covariances Rice quality traits Indica rice

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FACTOR ANALYSIS OF THE MAJOR AGRONOMIC traits IN SUNFLOWER

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生物数学学报 1994年第4期9卷 18-28页

作者： Qiao Chungui Zhao Jianwei Xie Jinfan Sun Yushu(Jilin Agricultural University,Changchun 130118,Jilin.Peoples Republic of China )(The Climatic Centre of Jilin Province,Changchun 130062,Jinn,People ’s Republic of China )

Factor analysis was conducted for the major agronomic traits in 1991 and 1992 field experiments with sunflower hybrids.The exper iment showed(1) the result of factor analysis differed with environments and hence special attention,should be paid to the practical utilization of it;(2) the conclusion of factor analysis had relative consistence to a certain extent in spite of the change in experiment materials and environments,which could then be used in guiding selection and evaluation of entries as well as in drawing up new breeding strategies.According to either year’s analysis,the original characters were decomposed into 4 inter-independent sets of traits known as common or main factors,among which factors of plant productivity,of nutritional growth power and of quality wereNo.4 Factor Analysis of the Major Agronomic traits… 19 relatively stable across years.If these factors do exist in sunflower populations,genetic improvement can be realised gradually for seed yield an quality factor by factor,which is expected to be more effective than independent selection on individual traits.

关键词： Sunflower agronomic traits factor analysis

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Restriction Fragment Length Polymorphism in the MC4R Gene and Its Genetic Effects on Carcass and Feather-down traits in Geese

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畜牧兽医学报 2009年第S1期40卷 13-17页

作者： CHEN Hong-quan HUANG Hua-yun CHEN Hua ZHANG Tong-yan School of Animal Science and Technology Anhui Agricultural University

Carcass,meat quality,and feather-down traits of 123 geese from an F_1 population of Wanxi White goose(male parent)and Sichuan White goose(female parent)were measured,and an additional 12 compound indices were constructed from the single traits,using factor analysis.The coding region of melanocortin receptor-4(MC4R)gene was amplified by PCR and the products were digested with four restriction endonucleases Hinf I,Ear I,Pst I,and Pvu II to detect restriction fragment length polymorphism(RFLP)in the MC4R gene,to analyze its associations with the traits.The only RFLP was exposed by digesting with Hinf I indicating two genotypes,HH and Hh,with frequencies of allele H and h being 0.8902 and 0.1098 in the F_1 population.Significant effects of genotype HH were found on carcass weight,eviscerated weight(with giblet),liver weight,heart weight,stomach percentage,abdominal fat percentage,breast muscle drip water loss and down proportion and many of the compound indices,and all genotypic contribution percentages(CP,genotypic effect on the population mean)were between-5%and 5%;effects of genotype Hh with the MC4R gene mutation,were not significant.Effects of genotype Hh were significant on two of the compound indices related to fat deposition:the fat index(CP=3.314%,P<0.05)and fatty acid quality(CP=1.218%,P<0.05).

关键词： goose MC4R gene RFLP economic traits

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Two awn-development-related peptides,GAD1 and OsEPFL2,promote seed dispersal and germination in rice

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Molecular Plant 2023年第3期16卷 485-488页

作者： Jing Jin Luling Xiong Julie E.Gray Bin Hu Chengcai Chu Guangdong Laboratory for Lingnan Modern Agriculture State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesCollege of AgricultureSouth China Agricultural UniversityGuangzhou 510642China Key Laboratory for Enhancing Resource Use Eficiency of Crops in South China Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhou510642China Guangdong Provincial Key Laboratory of Plant Molecular Breeding South China Agricultural UniversityGuangzhou 510642China Plants Photosynthesis and SoilSchool of BiosciencesUniversity of SheffieldSheffield S102TNUK

In nature,seed dispersal and germination are crucial for plant survival and propagation.Elaborate mechanisms have evolved that enhance the success of these events(Peart,1981;Bewley,1997),and the widespread distribution of grass species has been associated with the evolution of these traits.Many of these mechanisms are associated with characteristics that are intrinsic to the seed,such as awn development,seed shattering,and germination(Ntakirutimana et al.,2019).Awns and/or other seed appendages often help mature seeds to disperse widely and germinate under various challenging environments(Elbaum et al.,2007).

关键词： dispersal traits germination

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GenomeSyn:a bioinformatics tool for visualizing genome synteny and structural variations

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Journal of Genetics and Genomics 2022年第12期49卷 1174-1176页

作者： Zu-Wen Zhou Zhi-Guang Yu Xiao-Ming Huang Jin-Shen Liu Yi-Xiong Guo Ling-Ling Chen Jia-Ming Song State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources College of Life Science and TechnologyGuangxi UniversityNanningGuangxi 530004China College of Stomatology Guangxi Medical UniversityNanningGuangxi 530021China National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhanHubei 430070China

Advances in the next-generation and long-read sequencing technologies have promoted the development of genome-wide comparative genomics analysis,and constructing pangenomes and identifying structural variations(SVs)are becoming the frontier of genomics.Comparative genomics is of critical importance for determining the gene function and the evolutionary basis of traits.

关键词： traits Genome structural

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Kilobase-scale genomic deletion of DOTFL1 in Dendrobium orchids

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Journal of Genetics and Genomics 2022年第1期49卷 81-84页

作者： Yan Li Bin Zhang Hao Yu Department of Biological Sciences National University of Singapore14 Science Drive 4117543Singapore Temasek Life Sciences Laboratory 1 Research LinkNational University of Singapore 117604Singapore

Orchids make up one of the largest families of flowering plants(Orchidaceae) with a variety of ecological habitats and broad economic impact for their ornamental and medicinal values in the world.Sexual hybridization followed by the selection of attractive traits in progenies is a classical but dominant method for breeding new and improved orchid varieties. This method is typically time-consuming as most orchid genera possess a long vegetative phase that could last from one year to many years(Yu and Goh, 2001). Thus, the protracted breeding period so far remains a bottleneck for the rapid production of new orchid varieties to satisfy consumer appetites for desirable traits.

关键词： traits habitat breeding

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Cavefish as biological models in the laboratory and in the wild

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Zoological Research 2023年第4期44卷 834-836页

作者： William R.Jeffery Li Ma Ya-hui Zhao Department of Biology University of MarylandCollege ParkMD20742 USA Cave Fish Development and Evolution Research Group Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan650223China Institute of Zoology Chinese Academy of SciencesBeijing100101China

Cavefish have advanced to the forefront as excellent models for laboratory studies in developmental and evolutionary biology.The iconic Mexican characid,Astyanax mexicanus,which consists of a surface-dwelling morph and about 30 interfertile cave-dwelling morphs,has become a major contributor to behavior,sensory biology,trait evolution,and biomedicine(Jeffery,2020).There are about 200 scientifically-described cavefish species distributed in karst areas on most continents(Proudlove,2015).Similar to A.mexicanus,a small subset of other cavefish taxa coupled with related surface-dwelling species are now serving as additional laboratory models to address a variety of important biological problems.A prime example is the cyprinid genus Sinocycloceilus,which contains 75 closely related surface and cave species endemic to the karst massifs of southwestern China(Jiang et al.,2019,2023;Ma et al.,2019).Comparative studies of Chinese and Mexican cavefish can be used to address a host of questions concerning the convergence and divergence of cave related traits.In the future,other Chinese cavefish species,such as the cave loach,as well as the more recently discovered European cavefishes,are likely to join the current group of excellent laboratory models.This special issue of Zoological Research presents the results of current research on these diverse cavefish species.In addition to recent research using cavefish models in laboratory studies,this issue also covers new research on cavefish in the wild.

关键词： species fish traits

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